READemption-0.2.0.zip (63.71 kB)

READemption

Version 4 2014-07-22, 06:28

Version 3 2014-07-22, 06:28

Version 2 2014-03-30, 10:00

Version 1 2014-03-28, 12:33

software

posted on 2014-03-30, 10:00 authored by Konrad U. FörstnerKonrad U. Förstner, Jörg Vogel, Cynthia. Sharma

This is the v0.2.0 the tool READemption. Please visit the following web site for current versions and documentation:

https://github.com/konrad/READemption

http://pythonhosted.org/reademption

The READemption is a pipeline for the computational evaluation of RNA-Seq data. It was originally developed at the IMIB/ZINF to process dRNA-Seq reads (as introduced by Sharma et al., Nature, 2010 originating from bacterial samples. Meanwhile is has been extended to process data generated in different experimental setups and originating from all domains of life and is under active development. The subcommands which are provided by command-line interface cover read processing and aligning, coverage plot generation, gene expression quantification as well as differential gene expression analysis. READemption was applied to analyze numerous data sets. In order to set up analyses quickly READemption follows the principal of "convention over configuration": Once the input files are copied into defined folders no further parameters have to be given. Still, READemption's behavior can be adapted to specific needs of the user.